Evaluation of monocot and eudicot divergence using the sugarcane transcriptome(1[w])

Over 40,000 sugarcane (Saccharum officinarum) consensus sequences assembled from 237,954 expressed sequence tags were compared with the protein and DNA sequences from other angiosperms, including the genomes of Arabidopsis and rice (Oryza sativa). Approximately two-thirds of the sugarcane transcriptome have similar sequences in Arabidopsis. These sequences may represent a core set of proteins or protein domains that are conserved among monocots and eudicots and probably encode for essential angiosperm. functions. The remaining sequences represent putative monocot-specific genetic material, one-half of which were found only in sugarcane. These monocot-specific cDNAs represent either novelties or, in many cases, fast-evolving sequences that diverged substantially from their eudicot homologs. The wide comparative genome analysis presented here provides information on the evolutionary changes that underlie the divergence of monocots and eudicots. Our comparative analysis also led to the identification of several not yet annotated putative genes and possible gene loss events in Arabidopsis.

The Pediatric Rheumatology International Trials Organization American-College-of-Rheumatology provisional criteria for the evaluation of response to therapy in juvenile systemic lupus erythematosus: Prospective validation of the definition of improvement

Objective. To use the Pediatric Rheumatology International Trials Organization (PRINTO) core set of outcome measures to develop a validated definition of improvement for the evaluation of response to therapy in juvenile systemic lupus erythematosus (SLE).Methods. Thirty-seven experienced pediatric rheumatologists from 27 countries, each of whom had specific experience in the assessment of juvenile SLE patients, achieved consensus on 128 patient profiles as being clinically improved or not improved. Using the physicians' consensus ratings as the gold standard measure, the chi-square, sensitivity, specificity, false-positive and false-negative rates, area under the receiver operating characteristic curve, and kappa level of agreement for 597 candidate definitions of improvement were calculated. Only definitions with a kappa value greater than 0.7 were retained. The top definitions were selected based on the product of the content validity score multiplied by its kappa statistic.Results. The definition of improvement with the highest final score was at least 50% improvement from baseline in any 2 of the 5 core set measures, with no more than 1 of the remaining worsening by more than 30%.Conclusion. PRINTO proposes a valid and reproducible definition of improvement that reflects well the consensus rating of experienced clinicians and that incorporates clinically meaningful change in core set measures in a composite end point for the evaluation of global response to therapy in patients with juvenile SLE. The definition is now proposed for use in juvenile SLE clinical trials and may help physicians to decide whether a child with SLE responded adequately to therapy.

Inquérito sobre a qualidade de vida relacionada à saúde em crianças e adolescentes portadores de artrites idiopáticas juvenis

Objective: to study the impact of chronic arthritis on health related quality of life by means of two self-reported tools: the parents' version of the Childhood Health Assessment Questionnaire (CHAQ) and the Childhood Health Questionnaire PF50® (CHQ). Methods: both tools were filled in after proper instructions by 36 parents, during 1-2 clinic visits. The Disability Index (CHAQ) and the Physical and Psychosocial scores (CHQ) were compared to the core set of outcome measures, namely 1) physician's global assessment, 2) parents' global assessment, both scored by 10 cm visual analogue scale, 3) number of joints with active arthritis, 4) number of joints with limited range of motion, 5) erythrocyte sedimentation rate. Results: there was significant difference for all measures of disease activity, being higher in the polyarticular as compared to oligoarticular except for erythrocyte sedimentation rate, parents' global assessment, and psychosocial score. This leads to different parents' perceptions of disease activity and outcome. The responsiveness of the outcome measures during two follow-up visits of patients receiving active treatment indicated better responsiveness of physicians' global assessment among the subjective measures, and intermediate responsiveness of the self-reported measures in comparison to the number of active and limited joints, and erythrocyte sedimentation rate. Conclusions: the responsiveness of two health related quality of life tools indicates their relative sensitivity for assessing clinical improvement during active treatment in Juvenile Idiopathic Arthritis patients. Copyright © 2003 by Sociedade Brasileira de Pediatria.

The global information society: a statistical view

Includes bibliography

Inquérito sobre a qualidade de vida relacionada à saúde em crianças e adolescentes portadores de artrites idiopáticas juvenis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Designing Software Product Lines for Testability

Software product line (SPL) engineering offers several advantages in the development of families of software products such as reduced costs, high quality and a short time to market. A software product line is a set of software intensive systems, each of which shares a common core set of functionalities, but also differs from the other products through customization tailored to fit the needs of individual groups of customers. The differences between products within the family are well-understood and organized into a feature model that represents the variability of the SPL. Products can then be built by generating and composing features described in the feature model. Testing of software product lines has become a bottleneck in the SPL development lifecycle, since many of the techniques used in their testing have been borrowed from traditional software testing and do not directly take advantage of the similarities between products. This limits the overall gains that can be achieved in SPL engineering. Recent work proposed by both industry and the research community for improving SPL testing has begun to consider this problem, but there is still a need for better testing techniques that are tailored to SPL development. In this thesis, I make two primary contributions to software product line testing. First I propose a new definition for testability of SPLs that is based on the ability to re-use test cases between products without a loss of fault detection effectiveness. I build on this idea to identify elements of the feature model that contribute positively and/or negatively towards SPL testability. Second, I provide a graph based testing approach called the FIG Basis Path method that selects products and features for testing based on a feature dependency graph. This method should increase our ability to re-use results of test cases across successive products in the family and reduce testing effort. I report the results of a case study involving several non-trivial SPLs and show that for these objects, the FIG Basis Path method is as effective as testing all products, but requires us to test no more than 24% of the products in the SPL.

Towards global consensus on outcome measures for atopic eczema research: results of the HOME II meeting

The use of nonstandardized and inadequately validated outcome measures in atopic eczema trials is a major obstacle to practising evidence-based dermatology. The Harmonising Outcome Measures for Eczema (HOME) initiative is an international multiprofessional group dedicated to atopic eczema outcomes research. In June 2011, the HOME initiative conducted a consensus study involving 43 individuals from 10 countries, representing different stakeholders (patients, clinicians, methodologists, pharmaceutical industry) to determine core outcome domains for atopic eczema trials, to define quality criteria for atopic eczema outcome measures and to prioritize topics for atopic eczema outcomes research. Delegates were given evidence-based information, followed by structured group discussion and anonymous consensus voting. Consensus was achieved to include clinical signs, symptoms, long-term control of flares and quality of life into the core set of outcome domains for atopic eczema trials. The HOME initiative strongly recommends including and reporting these core outcome domains as primary or secondary endpoints in all future atopic eczema trials. Measures of these core outcome domains need to be valid, sensitive to change and feasible. Prioritized topics of the HOME initiative are the identification/development of the most appropriate instruments for the four core outcome domains. HOME is open to anyone with an interest in atopic eczema outcomes research.

Diagnostic criteria for hematopoietic stem cell transplant-associated microangiopathy: results of a consensus process by an International Working Group

BACKGROUND AND OBJECTIVES: There are no widely accepted criteria for the definition of hematopoietic stem cell transplant -associated microangiopathy (TAM). An International Working Group was formed to develop a consensus formulation of criteria for diagnosing clinically significant TAM. DESIGN AND METHODS: The participants proposed a list of candidate criteria, selected those considered necessary, and ranked those considered optional to identify a core set of criteria. Three obligatory criteria and four optional criteria that ranked highest formed a core set. In an appropriateness panel process, the participants scored the diagnosis of 16 patient profiles as appropriate or not appropriate for TAM. Using the experts' ratings on the patient profiles as a gold standard, the sensitivity and specificity of 24 candidate definitions of the disorder developed from the core set of criteria were evaluated. A nominal group technique was used to facilitate consensus formation. The definition of TAM with the highest score formed the final PROPOSAL. RESULTS: The Working Group proposes that the diagnosis of TAM requires fulfilment of all of the following criteria: (i) >4% schistocytes in blood; (ii) de novo, prolonged or progressive thrombocytopenia (platelet count <50 x 109/L or 50% or greater reduction from previous counts); (iii) sudden and persistent increase in lactate dehydrogenase concentration; (iv) decrease in hemoglobin concentration or increased transfusion requirement; and (v) decrease in serum haptoglobin. The sensitivity and specificity of this definition exceed 80%. INTERPRETATION AND CONCLUSIONS: The Working Group recommends that the presented criteria of TAM be adopted in clinical use, especially in scientific trials.

Identification of prognostic factors for chronicity in patients with low back pain: a review of screening instruments

Low back pain (LBP) is currently the most prevalent and costly musculoskeletal problem in modern societies. Screening instruments for the identification of prognostic factors in LBP may help to identify patients with an unfavourable outcome. In this systematic review screening instruments published between 1970 and 2007 were identified by a literature search. Nine different instruments were analysed and their different items grouped into ten structures. Finally, the predictive effectiveness of these structures was examined for the dependent variables including "work status", "functional limitation", and "pain". The strongest predictors for "work status" were psychosocial and occupational structures, whereas for "functional limitation" and "pain" psychological structures were dominating. Psychological and occupational factors show a high reliability for the prognosis of patients with LBP. Screening instruments for the identification of prognostic factors in patients with LBP should include these factors as a minimum core set.

Strengthening the food systems governance evidence base: Supporting commensurability of research through a systematic review of methods

Governance of food systems is a poorly understood determinant of food security. Much scholarship on food systems governance is non-empirical, while existing research is often case study-based and theoretically and methodologically incommensurable. This frustrates aggregation of evidence and generalisation. We undertook a systematic review of methods used in food systems governance research with a view to identifying a core set of indicators for future research. We gathered literature through a structured consultation and sampling from recent reviews. Indicators were identified and classified according to the levels and sectors they investigate. We found a concentration of indicators in food production at local to national levels and a sparseness in distribution and consumption. Unsurprisingly, many indicators of institutional structure were found, while agency-related indicators are moderately represented. We call for piloting and validation of these indicators and for methodological development to fill gaps identified. These efforts are expected to support a more consolidated future evidence base and eventual meta-analysis.

The emergence of the social determinants of health on the policy agenda in Britain: A case study, 1980--2003

Numerous theories have been advanced in the effort to explain how a given policy issue manages to take root in the public sphere and subsequently move forward on the public legislative agenda—or not. This study examined how the social determinants of health (SDOH) came to be part of the legislative policy agenda in Britain from 1980 to 2003. ^ The specific objectives of the research were: (1) to conduct a sociopolitical analysis grounded in alternative agenda-setting theories to identify the factors responsible for moving the social determinants health perspective onto the British policy agenda; and (2) to determine which of the theories and related dimensions best accounted for the emergence of this perspective. ^ A triangulated content and context analysis of British news articles, historical accounts, and research commentaries of the SDOH movement was conducted guided by relevant agenda-setting theories set within a social movement framework to chronicle the emergence of the SDOH as a significant policy issue in Britain. ^ The most influential social movement and agenda setting elements in the emergence of the SDOH in Britain were issue generation tactics, framing efforts, mobilizing structures, and political opportunities grounded in social movement and agenda setting theories. Policy content or the details of the policy had comparatively little impact on the successful emergence of the SDOH. Despite resistance by the government, from 1980 to 1996 interest groups created a political understanding of the SDOH utilizing a framing package encompassing notions of inequality, fairness, and justice. This frame transmitted a powerful idea connected to a core set of British values and beliefs. After 1996, a shift in political opportunities cemented the institutional arrangements needed to sustain an environment conducive to the development and implementation of SDOH policies and programs. ^ This research demonstrates that the U.S. emergence of the SDOH on the policy agenda will depend upon: (1) U.S. ideals and values regarding poverty, inequality, race, health, and health care that will determine issue framing; (2) political opportunities that will emerge—or not—to advance the SDOH policy agenda; and (3) the mobilizing structures that support or oppose the issue. ^

Optimización de la composición del hueco de fachada en materia de eficiencia energética. Propuesta de indicador como herramienta para el análisis integral del elemento acristalado = Energy performance optimization of window systems. Proposal of an indicator as a tool for an integrated analysis of glazing

La hipótesis de esta tesis es: "La optimización de la ventana considerando simultáneamente aspectos energéticos y aspectos relativos a la calidad ambiental interior (confort higrotérmico, lumínico y acústico) es compatible, siempre que se conozcan y consideren las sinergias existentes entre ellos desde las primeras fases de diseño". En la actualidad se desconocen las implicaciones de muchas de las decisiones tomadas en torno a la ventana; para que su eficiencia en relación a todos los aspectos mencionados pueda hacerse efectiva es necesaria una herramienta que aporte más información de la actualmente disponible en el proceso de diseño, permitiendo así la optimización integral, en función de las circunstancias específicas de cada proyecto. En la fase inicial de esta investigación se realiza un primer acercamiento al tema, a través del estado del arte de la ventana; analizando la normativa existente, los componentes, las prestaciones, los elementos experimentales y la investigación. Se observa que, en ocasiones, altos requisitos de eficiencia energética pueden suponer una disminución de las prestaciones del sistema en relación con la calidad ambiental interior, por lo que surge el interés por integrar al análisis energético aspectos relativos a la calidad ambiental interior, como son las prestaciones lumínicas y acústicas y la renovación de aire. En este punto se detecta la necesidad de realizar un estudio integral que incorpore los distintos aspectos y evaluar las sinergias que se dan entre las distintas prestaciones que cumple la ventana. Además, del análisis de las soluciones innovadoras y experimentales se observa la dificultad de determinar en qué medida dichas soluciones son eficientes, ya que son soluciones complejas, no caracterizadas y que no están incorporadas en las metodologías de cálculo o en las bases de datos de los programas de simulación. Por lo tanto, se plantea una segunda necesidad, generar una metodología experimental para llevar a cabo la caracterización y el análisis de la eficiencia de sistemas innovadores. Para abordar esta doble necesidad se plantea la optimización mediante una evaluación del elemento acristalado que integre la eficiencia energética y la calidad ambiental interior, combinando la investigación teórica y la investigación experimental. En el ámbito teórico, se realizan simulaciones, cálculos y recopilación de información de distintas tipologías de hueco, en relación con cada prestación de forma independiente (acústica, iluminación, ventilación). A pesar de haber partido con un enfoque integrador, resulta difícil esa integración detectándose una carencia de herramientas disponible. En el ámbito experimental se desarrolla una metodología para la evaluación del rendimiento y de aspectos ambientales de aplicación a elementos innovadores de difícil valoración mediante la metodología teórica. Esta evaluación consiste en el análisis comparativo experimental entre el elemento innovador y un elemento estándar; para llevar a cabo este análisis se han diseñado dos espacios iguales, que denominamos módulos de experimentación, en los que se han incorporado los dos sistemas; estos espacios se han monitorizado, obteniéndose datos de consumo, temperatura, iluminancia y humedad relativa. Se ha realizado una medición durante un periodo de nueve meses y se han analizado y comparado los resultados, obteniendo así el comportamiento real del sistema. Tras el análisis teórico y el experimental, y como consecuencia de esa necesidad de integrar el conocimiento existente se propone una herramienta de evaluación integral del elemento acristalado. El desarrollo de esta herramienta se realiza en base al procedimiento de diagnóstico de calidad ambiental interior (CAI) de acuerdo con la norma UNE 171330 “Calidad ambiental en interiores”, incorporando el factor de eficiencia energética. De la primera parte del proceso, la parte teórica y el estado del arte, se obtendrán los parámetros que son determinantes y los valores de referencia de dichos parámetros. En base a los parámetros relevantes obtenidos se da forma a la herramienta, que consiste en un indicador de producto para ventanas que integra todos los factores analizados y que se desarrolla según la Norma UNE 21929 “Sostenibilidad en construcción de edificios. Indicadores de sostenibilidad”. ABSTRACT The hypothesis of this thesis is: "The optimization of windows considering energy and indoor environmental quality issues simultaneously (hydrothermal comfort, lighting comfort, and acoustic comfort) is compatible, provided that the synergies between these issues are known and considered from the early stages of design ". The implications of many of the decisions made on this item are currently unclear. So that savings can be made, an effective tool is needed to provide more information during the design process than the currently available, thus enabling optimization of the system according to the specific circumstances of each project. The initial phase deals with the study from an energy efficiency point of view, performing a qualitative and quantitative analysis of commercial, innovative and experimental windows. It is observed that sometimes, high-energy efficiency requirements may mean a reduction in the system's performance in relation to user comfort and health, that's why there is an interest in performing an integrated analysis of indoor environment aspects and energy efficiency. At this point a need for a comprehensive study incorporating the different aspects is detected, to evaluate the synergies that exist between the various benefits that meet the window. Moreover, from the analysis of experimental and innovative windows, a difficulty in establishing to what extent these solutions are efficient is observed; therefore, there is a need to generate a methodology for performing the analysis of the efficiency of the systems. Therefore, a second need arises, to generate an experimental methodology to perform characterization and analysis of the efficiency of innovative systems. To address this dual need, the optimization of windows by an integrated evaluation arises, considering energy efficiency and indoor environmental quality, combining theoretical and experimental research. In the theoretical field, simulations and calculations are performed; also information about the different aspects of indoor environment (acoustics, lighting, ventilation) is gathered independently. Despite having started with an integrative approach, this integration is difficult detecting lack available tools. In the experimental field, a methodology for evaluating energy efficiency and indoor environment quality is developed, to be implemented in innovative elements which are difficult to evaluate using a theoretical methodology This evaluation is an experimental comparative analysis between an innovative element and a standard element. To carry out this analysis, two equal spaces, called experimental cells, have been designed. These cells have been monitored, obtaining consumption, temperature, luminance and relative humidity data. Measurement has been performed during nine months and results have been analyzed and compared, obtaining results of actual system behavior. To advance this optimization, windows have been studied from the point of view of energy performance and performance in relation to user comfort and health: thermal comfort, acoustic comfort, lighting comfort and air quality; proposing the development of a methodology for an integrated analysis including energy efficiency and indoor environment quality. After theoretical and experimental analysis and as a result of the need to integrate existing knowledge, a comprehensive evaluation procedure for windows is proposed. This evaluation procedure is developed according to the UNE 171330 "Indoor Environmental Quality", also incorporating energy efficiency and cost as factors to evaluate. From the first part of the research process, outstanding parameters are chosen and reference values of these parameters are set. Finally, based on the parameters obtained, an indicator is proposed as windows product indicator. The indicator integrates all factors analyzed and is developed according to ISO 21929-1:2011"Sustainability in building construction. Sustainability indicators. Part 1: Framework for the development of indicators and a core set of indicators for buildings".

Gene content phylogeny of herpesviruses

Clusters of orthologous groups [COGs; Tatusov, R. L., Koonin, E. V. & Lipman, D. J. (1997) Science 278, 631–637] were identified for a set of 13 completely sequenced herpesviruses. Each COG represented a family of gene products conserved across several herpes genomes. These families were defined without using an arbitrary threshold criterion based on sequence similarity. The COG technique was modified so that variable stringency in COG construction was possible. High stringencies identify a core set of highly conserved genes. Varying COG stringency reveals differences in the degree of conservation between functional classes of genes. The COG data were used to construct whole-genome phylogenetic trees based on gene content. These trees agree well with trees based on other methods and are robust when tested by bootstrap analysis. The COG data also were used to construct a reciprocal tree that clustered genes with similar phylogenetic profiles. This clustering may give clues to genes with related functions or with related histories of acquisition and loss during herpesvirus evolution.

Viscosupplementation for the treatment of osteoarthritis of the knee (Review)

Background Osteoarthritis (OA) is the most prevalent chronic joint disorder worldwide and is associated with significant pain and disability. Objectives To assess the effects of viscosupplementation in the treatment of OA of the knee. The products were hyaluronan and hylan derivatives (Adant, Arthrum H, Artz (Artzal, Supartz), BioHy (Arthrease, Euflexxa, Nuflexxa), Durolane, Fermathron, Go-On, Hyalgan, Hylan G-F 20 (Synvisc Hylan G-F 20), Hyruan, NRD-101 (Suvenyl), Orthovisc, Ostenil, Replasyn, SLM-10, Suplasyn, Synject and Zeel compositum). Search strategy MEDLINE (up to January (week 1) 2006 for update), EMBASE, PREMEDLINE, Current Contents up to July 2003, and the Cochrane Central Register of Controlled Trials (CENTRAL) were searched. Specialised journals and reference lists of identified randomised controlled trials (RCTs) and pertinent review articles up to December 2005 were handsearched. Selection criteria RCTs of viscosupplementation for the treatment of people with a diagnosis of OA of the knee were eligible. Single and double-blinded studies, placebo-based and comparative studies were eligible. At least one of the four OMERACT III core set outcome measures had to be reported (Bellamy 1997). Data collection and analysis Each trial was assessed independently by two reviewers for its methodological quality using a validated tool. All data were extracted by one reviewer and verified by a second reviewer. Continuous outcome measures were analysed as weighted mean differences (WMD) with 95% confidence intervals (CI). However, where different scales were used to measure the same outcome, standardized mean differences (SMD) were used. Dichotomous outcomes were analyzed by relative risk (RR). Main results Seventy-six trials with a median quality score of 3 (range 1 to 5) were identified. Follow-up periods varied between day of last injection and eighteen months. Forty trials included comparisons of hyaluronan/hylan and placebo (saline or arthrocentesis), ten trials included comparisons of intra-articular (IA) corticosteroids, six trials included comparisons of nonsteroidal anti-inflammatory drugs (NSAIDs), three trials included comparisons of physical therapy, two trials included comparisons of exercise, two trials included comparisons of arthroscopy, two trials included comparisons of conventional treatment, and fifteen trials included comparisons of other hyaluronans/hylan. The pooled analyses of the effects of viscosupplements against 'placebo' controls generally supported the efficacy of this class of intervention. In these same analyses, differential efficacy effects were observed for different products on different variables and at different timepoints. Of note is the 5 to 13 week post injection period which showed a percent improvement from baseline of 28 to 54% for pain and 9 to 32% for function. In general, comparable efficacy was noted against NSAIDs and longer-term benefits were noted in comparisons against IA corticosteroids. In general, few adverse events were reported in the hyaluronan/hylan trials included in these analyses. Authors' conclusions Based on the aforementioned analyses, viscosupplementation is an effective treatment for OA of the knee with beneficial effects: on pain, function and patient global assessment; and at different post injection periods but especially at the 5 to 13 week post injection period. It is of note that the magnitude of the clinical effect, as expressed by the WMD and standardised mean difference (SMD) from the RevMan 4.2 output, is different for different products, comparisons, timepoints, variables and trial designs. However, there are few randomised head-to-head comparisons of different viscosupplements and readers should be cautious, therefore, in drawing conclusions regarding the relative value of different products. The clinical effect for some products, against placebo, on some variables at some timepoints is in the moderate to large effect-size range. Readers should refer to relevant tables to review specific detail given the heterogeneity in effects across the product class and some discrepancies observed between the RevMan 4.2 analyses and the original publications. Overall, the analyses performed are positive for the HA class and particularly positive for some products with respect to certain variables and timepoints, such as pain on weight bearing at 5 to 13 weeks postinjection. In general, sample-size restrictions preclude any definitive comment on the safety of the HA class of products; however, within the constraints of the trial designs employed no major safety issues were detected. In some analyses viscosupplements were comparable in efficacy to systemic forms of active intervention, with more local reactions but fewer systemic adverse events. In other analyses HA products had more prolonged effects than IA corticosteroids. Overall, the aforementioned analyses support the use of the HA class of products in the treatment of knee OA.

Evaluation of WOMAC 20, 50, 70 response criteria in patients treated with hylan G-F 20 for knee osteoarthritis

Objective: A secondary analysis of a previously conducted one year randomised controlled trial to evaluate the capacity of responder criteria based on the WOMAC index to detect between treatment group differences. Methods: 255 patients with knee osteoarthritis were randomised to appropriate care with hylan G-F 20'' (AC+H) or appropriate care without hylan G-F 20'' (AC). In the original analysis, two definitions of patient response from baseline to month 12 were used: ( 1) at least a 20% reduction in WOMAC pain score ( WOMAC 20P); ( 2) at least a 20% reduction in WOMAC pain score and at least a 20% reduction in either WOMAC function or stiffness score ( WOMAC 20PFS). For this analysis, a responder was identified using 50% and 70% minimum clinically important response levels to investigate how increasing response affects the ability to detect treatment group differences. Results: The hylan G- F 20 group had numerically more responders using all patient responder criteria. Increasing the response level from 20% to 50% detected similar differences between treatment groups (25% to 29%). Increasing the response level to 70% reduced the differences between treatment groups (11% to 12%) to a point where the differences were not significant after Bonferroni adjustment. Conclusions: These results provide evidence for incorporating response levels ( WOMAC 50) in clinical trials. While differences at the highest threshold ( WOMAC 70) were not statistically detectable, an appropriately powered study may be capable of detecting differences even at this very high level of improvement.